人类基因参考基因组中的2500多个编码基因仍然存在不确定的状态
Miguel Maquedano1, Daniel Cerdán-Vélez1, Michael L Tress1
1Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO).
bioRxiv : the preprint server for biology
|December 23, 2024
概括
人类蛋白质组注释仍然不一致,主要数据库在数千个编码基因状态上存在分歧. 超过2000个基因显示潜在的非编码特征,这表明对真正的蛋白质编码基因的高估.
科学领域:
- 基因组学就是基因组学.
- 蛋白质组学是指蛋白质组学.
- 生物信息学是一种生物信息学.
背景情况:
- 人类蛋白质组注释依赖于主要数据库,如Ensembl/GENCODE,RefSeq和UniProtKB.
- 2018年之前的分析揭示了这些数据库之间关于人类基因编码状态的重大分歧.
研究的目的:
- 用更新的数据集重新评估人类蛋白质组注释在Ensembl/GENCODE,RefSeq和UniProtKB中的一致性.
- 在注释编码基因组中识别和分析具有潜在非编码特征的基因.
主要方法:
- 从Ensembl/GENCODE,RefSeq和UniProtKB.B.中对更新的基因注释进行比较分析.
- 检查了21,873个编码基因,使用了8个特征表明非编码基因特征.
- 排除读透基因和免疫球蛋白片段基因,以进行精细的比较.
主要成果:
- 尽管有更新,但仍然存在显著的差异,有2,606个注释的基因具有有争议的编码状态.
- 在2018年和目前的分析之间,超过700个基因被合并或重新分类.
- 标注为编码的2000多个基因表现出特征,表明它们可能是非编码或伪基因.
结论:
- 人类蛋白质组注释数据库在基因编码状态上仍然存在重大分歧.
- 许多被认为是编码的基因实际上可能是非编码的或伪基因.
- 目前的注释实践可能高估了蛋白质编码基因的真实数量.
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